After complete sequencing of its genome and annotation of the majority of its ~32,000 genes, rice genome has become the model genome among the cereal genomes, and the focus has shifted from structural to functional genomics and application of genomic-derived information in rice breeding. During the past 2 decades, intensive worldwide efforts have led to significant improvements in rice. An abundance of molecular markers and information related to many genes/quantitative trait loci that control agronomically important traits such as yield, quality, and biotic and abiotic stress tolerance have been identified. Bridging the application gap between quantitative trait locus identification and marker-assisted selection breeding is an urgent, arduous, and long-term task. Marker development, allele mining, gene discovery, and molecular breeding have progressed to a great extent because of the rapid development of next-generation sequencing, large-scale high-density genotyping, and genome-wide selection strategies. The availability of high-density markers and the rapidly decreasing cost of genotyping have facilitated marker-assisted selection of many traits that were previously not possible.